A critical evaluation of automatic atom mapping algorithms and tools

The identification of the atoms which change their position in chemical reactions is an important knowledge within the field of Metabolic Engineering. This can lead to new advances at different levels from the reconstruction of metabolic networks to the classification of chemical reactions, through the identification of the atomic changes inside a reaction. The Atom Mapping approach was initially developed in the 1960s, but recently suffered important advances, being used in diverse biological and biotechnological studies. The main methodologies used for atom mapping are the Maximum Common Substructure and the Linear Optimization methods, which both require computational know-how and powerful resources to run the underlying tools. In this work, we assessed a number of previously implemented atom mapping frameworks, and built a framework able of managing the different data inputs and outputs, as well as the mapping process provided by each of these third-party tools. We evaluated the admissibility of the calculated atom maps from different algorithms, also assessing if with different approaches we were capable of returning equivalent atom maps for the same chemical reaction.ERDF -European Regional Development Fund(UID/BIO/04469/2013)info:eu-repo/semantics/publishedVersio

Fixed-time artificial insemination in beef cattle

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: The study was designed to test the effect of fixed-time artificial insemination (fixed-AI) after the slightly modified Ovsynch protocol on the pregnancy rate in beef cattle in Finnish field conditions. The modification was aimed to optimize the number of offsprings per AI dose. Methods: Ninety Charolais cows and heifers were entered into the program an average of 1.8 times. Thus, 164 animal cases were included. Animals were administered 10-12 μg of buserelin. Seven days later animals without a corpus luteum (CL) were rejected (20.7%) while the remaining 130 cases with a CL were administered prostaglandin F2α, followed 48 h later with a second injection of buserelin (8-10 μg). Fixed-AI was performed 16-20 hours after the last injection. Results: The pregnancy rate was 51.5 % (67/130). The pregnancy rate after a short interval (50-70 d) from calving to entering the program was significantly higher than that after a long interval (>70 d). Conclusion: This protocol seems to give acceptable pregnancy results in beef herds and its effect on saving labour is notable

Vitamin D supplementation and breast cancer prevention : a systematic review and meta-analysis of randomized clinical trials

In recent years, the scientific evidence linking vitamin D status or supplementation to breast cancer has grown notably. To investigate the role of vitamin D supplementation on breast cancer incidence, we conducted a systematic review and meta-analysis of randomized controlled trials comparing vitamin D with placebo or no treatment. We used OVID to search MEDLINE (R), EMBASE and CENTRAL until April 2012. We screened the reference lists of included studies and used the “Related Article” feature in PubMed to identify additional articles. No language restrictions were applied. Two reviewers independently extracted data on methodological quality, participants, intervention, comparison and outcomes. Risk Ratios and 95% Confident Intervals for breast cancer were pooled using a random-effects model. Heterogeneity was assessed using the I2 test. In sensitivity analysis, we assessed the impact of vitamin D dosage and mode of administration on treatment effects. Only two randomized controlled trials fulfilled the pre-set inclusion criteria. The pooled analysis included 5372 postmenopausal women. Overall, Risk Ratios and 95% Confident Intervals were 1.11 and 0.74–1.68. We found no evidence of heterogeneity. Neither vitamin D dosage nor mode of administration significantly affected breast cancer risk. However, treatment efficacy was somewhat greater when vitamin D was administered at the highest dosage and in combination with calcium (Risk Ratio 0.58, 95% Confident Interval 0.23–1.47 and Risk Ratio 0.93, 95% Confident Interval 0.54–1.60, respectively). In conclusions, vitamin D use seems not to be associated with a reduced risk of breast cancer development in postmenopausal women. However, the available evidence is still limited and inadequate to draw firm conclusions. Study protocol code: FARM8L2B5L

Age-Related Declines in Lower Limb Muscle Function are Similar in Power and Endurance Athletes of Both Sexes: A Longitudinal Study of Master Athletes

The age-related decline in muscle function, particularly muscle power, is associated with increased risk of important clinical outcomes. Physical activity is an important determinant of muscle function, and different types of physical activity e.g. power-based versus endurance-based exercise appear to have differential effects on muscle power. Cross-sectional studies suggest that participation in power-based exercise is associated with greater muscle power across adulthood but this has not been investigated longitudinally. We recruited eighty-nine male and female power and endurance master athletes (sprint and distance runners respectively, baseline age 35–90y). Using jumping mechanography, we measured lower limb muscle function during a vertical jump including at least two testing sessions longitudinally over 4.5 ± 2.4y. We examined effects of time, discipline (power/endurance) and sex in addition to two- and three-way interactions using linear mixed-effects models. Peak relative power, relative force and jump height, but not Esslingen Fitness Index (indicating peak power relative to sex and age-matched reference data) declined with time. Peak power, force, height and EFI were greater in power than endurance athletes. There were no sex, discipline or sex*discipline interactions with time for any variable, suggesting that changes were similar over time for athletes of both sexes and disciplines. Advantages in lower limb muscle function in power athletes were maintained with time, in line with previous cross-sectional studies. These results suggest that improvements in lower limb function in less active older individuals following power-based training persist with continued adherence, although this requires further investigation in interventional studies

Electroosmotically generated disinfectant from urine as a by-product of electricity in microbial fuel cell for the inactivation of pathogenic species

This work presents a small scale and low cost ceramic based microbial fuel cell, utilising human urine into electricity, while producing clean catholyte into an initially empty cathode chamber through the process of electro-osmostic drag. It is the first time that the catholyte obtained as a by-product of electricity generation from urine was transparent in colour and reached pH>13 with high ionic conductivity values. The catholyte was collected and used ex situ as a killing agent for the inactivation of a pathogenic species such as Salmonella typhimurium, using a luminometer assay. Results showed that the catholyte solutions were efficacious in the inactivation of the pathogen organism even when diluted up to 1:10, resulting in more than 5 log-fold reduction in 4 min. Long-term impact of the catholyte on the pathogen killing was evaluated by plating Salmonella typhimurium on agar plates and showed that the catholyte possesses a long-term killing efficacy and continued to inhibit pathogen growth for 10 days

A case–control study of selenium in nails and prostate cancer risk in British men

In view of the experimental evidence suggesting that the micronutrient selenium reduces prostate cancer risk, we investigated the association between the selenium level in fingernails, a measure of long-term selenium intake, and prostate cancer risk in a case-control study among 656 British men, conducted in 1989-1992. Nail clippings were taken at the time of recruitment and selenium concentration, measured using neutron activation techniques, was successfully assayed for 300 case-control pairs and varied six-fold among the controls (0.59 p.p.m.; interquartile range, 0.50-0.71 p.p.m.). Nail selenium concentration was not significantly associated with prostate cancer risk: men in the highest quartile of nail selenium had a slightly increased risk compared with men in the lowest quartile (OR 1.24, 95 CI, 0.73-2.10); for advanced prostate cancer, men in the highest quartile had a slightly reduced risk compared with men in the lowest quartile (OR 0.78, 95% CI, 0.27-2.25). These results suggest that selenium is not strongly associated with prostate cancer risk in British men

Factors associated with low bone mass in the hemodialysis patients – a cross-sectional correlation study

<p>Abstract</p> <p>Background</p> <p>Low bone mass is common in end-stage renal disease patients, especially those undergoing hemodialysis. It can lead to serious bone health problems such as fragility fractures. The purpose of this study is to investigate the risk factors of low bone mass in the hemodialysis patients.</p> <p>Methods</p> <p>Sixty-three subjects on hemodialysis for at least 6 months were recruited from a single center for this cross-sectional study. We collected data by questionnaire survey and medical records review. All subjects underwent a bone mineral density (BMD) assay with dual-energy x-ray absorptiometry at the lumbar spine and right hip. Data were statistically analyzed by means of descriptive analysis, independent t test and one way analysis of variance for continuous variables, Pearson product-moment correlation to explore the correlated factors of BMD, and stepwise multiple linear regression to identify the predictors of low bone mass.</p> <p>Results</p> <p>Using WHO criteria as a cutoff point, fifty-one subjects (81%) had a T-score lower than -1, of them 8 subjects (13%) had osteoporosis with the femoral neck most commonly affected. Regarding risk factors, age, serum alkaline phosphatase (ALP) level, and intact parathyroid hormone (iPTH) level had significant negative correlations with the femoral neck and lumbar spine BMD. On the other hand, serum albumin level, effective exercise time, and body weight (BW) had significant positive correlations with the femoral neck and lumbar spine BMD. Age, effective exercise time, and serum albumin level significantly predicted the femoral neck BMD (R²× 0.25), whereas BW and the ALP level significantly predicted the lumbar spine BMD (R²× 0.20).</p> <p>Conclusion</p> <p>This study showed that advanced age, low BW, low serum albumin level, and high ALP and iPTH levels were associated with a low bone mass in the hemodialysis patients. We suggest that regular monitoring of the femoral neck BMD, maintaining an adequate serum albumin level and BW, and undertaking an exercise program are important to improve bone health in the patients undergoing hemodialysis.</p

Food venue choice, consumer food environment, but not food venue availability within daily travel patterns are associated with dietary intake among adults, Lexington Kentucky 2011

Objective The retail food environment may be one important determinant of dietary intake. However, limited research focuses on individuals’ food shopping behavior and activity within the retail food environment. This study’s aims were to determine the association between six various dietary indicators and 1) food venue availability; 2) food venue choice and frequency; and 3) availability of healthy food within food venue. Methods In Fall, 2011, a cross-sectional survey was conducted among adults (n=121) age 18 years and over in Lexington, Kentucky. Participants wore a global position system (GPS) data logger for 3-days (2 weekdays and 1 weekend day) to track their daily activity space, which was used to assess food activity space. They completed a survey to assess demographics, food shopping behaviors, and dietary outcomes. Food store audits were conducted using the Nutrition Environment Measurement Survey-Store Rudd (NEMS-S) in stores where respondents reported purchasing food (n=22). Multivariate logistic regression was used to examine associations between six dietary variables with food venue availability within activity space; food venue choice; frequency of shopping; and availability of food within food venue. Results 1) Food venue availability within activity space – no significant associations. 2) Food Venue Choice – Shopping at farmers’ markets or specialty grocery stores reported higher odds of consuming fruits and vegetables (OR 1.60 95% CI [1.21, 2.79]). Frequency of shopping - Shopping at a farmers’ markets and specialty stores at least once a week reported higher odds of consumption of fruits and vegetables (OR 1.55 95% CI [1.08, 2.23]). Yet, shopping frequently at a super market had higher odds of consuming sugar-sweetened beverages (OR 1.39 95% CI [1.03, 1.86]). 3) Availability of food within store – those who shop in supermarkets with high availability of healthy food has lower odds of consuming sugar-sweetened beverages (OR 0.65 95% CI [0.14, 0.83]). Conclusion Interventions aimed at improving fruit and vegetable intake need to consider where individuals’ purchase food and the availability within stores as a behavioral and environmental strategy